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nextflow.config
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nextflow.config
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// Load processes parameters
includeConfig 'conf/base.config'
// Load resources configuration
includeConfig 'conf/resources.config'
// Export Time Zone required for QIIME2 2019.10
env {
TZ = 'Europe/Paris'
}
manifest {
name = 'samba'
author = 'IFREMER-IRSI-SeBiMER'
description = 'Standardized and Automated MetaBarcoding Analyses workflow developped by Ifremer SeBiMER team'
homePage = 'https://github.com/ifremer-bioinformatics/samba'
mainScript = 'main.nf'
nextflowVersion = '>=20.04.1'
version = 'v3.1.0'
}
// Execution profiles
profiles {
shortreadstest {
includeConfig 'conf/shortreadstest.config'
includeConfig 'conf/reports.config'
// Workdir for temporary data
workDir = "${baseDir}/work/$params.projectName"
}
longreadstest {
includeConfig 'conf/longreadstest.config'
includeConfig 'conf/reports.config'
// Workdir for temporary data
workDir = "${baseDir}/work/$params.projectName"
}
custom {
includeConfig 'conf/custom.config'
includeConfig 'conf/reports.config'
// Workdir for temporary data
workDir = "${baseDir}/work/$params.projectName"
}
conda {
docker.enabled = false
singularity.enabled = false
createTimeout = '60min'
process {
withLabel : qiime2_env1cpu {
conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
}
withLabel : qiime2_env {
conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
}
withLabel : qiime2_highRAM {
conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
}
withLabel : microdecon_env {
conda = "${baseDir}/containers/microdecon-1.0.2/environment.yml"
}
withLabel : r_stats_env {
conda = "${baseDir}/containers/r-3.6.1/environment.yml"
}
withLabel : seqtk_env {
conda = "${baseDir}/containers/seqtk-1.2/environment.yml"
}
withLabel : jinja2_env {
conda = "${baseDir}/containers/jinja2-2.11.1/environment.yml"
}
withLabel : biopython_env {
conda = "${baseDir}/containers/biopython-1.79/environment.yml"
}
withLabel : lr_mapping_env {
container = "${baseDir}/containers/longreads-1.0/environment.yml"
}
}
}
docker {
docker {
enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
}
process {
withLabel : qiime2_env1cpu {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : qiime2_env {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : qiime2_highRAM {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : microdecon_env {
container = "sebimer/samba-microdecon:1.0.2"
}
withLabel : r_stats_env {
container = "sebimer/samba-r:3.6.1"
}
withLabel : seqtk_env {
container = "sebimer/samba-seqtk:1.2"
}
withLabel : jinja2_env {
container = "sebimer/samba-jinja2:2.11.1"
}
withLabel : biopython_env {
container = "sebimer/samba-v4-biopython:1.79"
}
withLabel : lr_mapping_env {
container = "sebimer/samba-longreads:1.0"
}
}
singularity.enabled = false
}
singularity {
docker.enabled = false
singularity.autoMounts = true
singularity.enabled = true
process {
withLabel : qiime2_env1cpu {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : qiime2_env {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : qiime2_highRAM {
container = "sebimer/samba-qiime2:2019.10"
}
withLabel : microdecon_env {
container = "sebimer/samba-microdecon:1.0.2"
}
withLabel : r_stats_env {
container = "sebimer/samba-r:3.6.1"
}
withLabel : seqtk_env {
container = "sebimer/samba-seqtk:1.2"
}
withLabel : jinja2_env {
container = "sebimer/samba-jinja2:2.11.1"
}
withLabel : biopython_env {
container = "sebimer/samba-v4-biopython:1.79"
}
withLabel : lr_mapping_env {
container = "sebimer/samba-longreads:1.0"
}
}
}
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}